7DN7

Crystal structure of ternary complexes of lactoperoxidase with hydrogen peroxide at 1.70 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QL6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	298	0.2M Ammonium Iodide, PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.92	α = 90
b = 79.498	β = 102.25
c = 77.723	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARRESEARCH	Mirror	2010-10-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97	ESRF	BM14

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.7	75.9	96	0.068	11	9.2		67857

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.74	96.2		0.33	5.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3ql6	1.7	26.707	66994	3384	94.999	0.183	0.1814	0.2043	29.047

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.018		0.014	-0.046		0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.542
r_dihedral_angle_4_deg	15.009
r_dihedral_angle_3_deg	13.885
r_lrange_other	10.287
r_lrange_it	10.286
r_dihedral_angle_1_deg	7.261
r_scangle_it	5.288
r_scangle_other	5.287
r_mcangle_it	5.049
r_mcangle_other	5.042
r_scbond_it	3.408
r_scbond_other	3.407
r_mcbond_it	3.159
r_mcbond_other	3.134
r_chiral_restr_other	2.966
r_angle_other_deg	2.561
r_angle_refined_deg	1.827
r_symmetry_nbd_refined	0.307
r_nbd_other	0.244
r_nbd_refined	0.22
r_symmetry_nbd_other	0.218
r_xyhbond_nbd_refined	0.211
r_symmetry_xyhbond_nbd_refined	0.193
r_nbtor_refined	0.174
r_symmetry_xyhbond_nbd_other	0.14
r_xyhbond_nbd_other	0.135
r_chiral_restr	0.097
r_metal_ion_refined	0.097
r_symmetry_nbtor_other	0.078
r_bond_other_d	0.034
r_symmetry_metal_ion_refined	0.034
r_gen_planes_other	0.02
r_bond_refined_d	0.012
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4770
Nucleic Acid Atoms
Solvent Atoms	659
Heterogen Atoms	138

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing